We combine classical molecular dynamics simulations and quantum density functional theory calculations to study the temperature effects on the electron affinity of the water octamer. The atomistic simulations provide a sample of the cluster's conformations as a function of the temperature, on which the density functional calculations are carried on. As the temperature increases, the cluster und...

In this paper a coarse-grained method called elastic network interpolation (ENI) is used to generate feasible transition pathways between two given conformations of the core central domain of 16S Ribosomal RNA (16S rRNA). The two given conformations are the extremes generated by a molecular dynamics (MD) simulation, which differ from each other by 10A in root-mean-square deviation (RMSD). It ta...

OmniMerge performs a systematic search to enumerate all conformations of a molecule (at a given level of torsionangle resolution) that satisfy a set of local geometric constraints. Constraints would typically come from NMR experiments, but applications such as docking or homology modeling could also give rise to similar constraints. The molecule to be searched is partitioned into small subchain...